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ID method for Oly gonad diff. methylation analysis #166

Closed laurahspencer closed 6 years ago

laurahspencer commented 6 years ago

Need to determine which method to use to measure diff. methylation in my Oly samples. I am preparing 16 samples total (8 per treatment), but might not run them all. I currently am not planning on targeting any genes, rather using the analysis to ID global differences and diff. methylated regions.

What method is reasonable? I thought RRBS might be an option but according to Kurdyukov 2016 it's $2500/sample. I see Jay used EpiRadSeq on ~25 samples and was able to obtain SNP data, too. Jiang 2016 paper looked at gigas methylation between parent/offspring via fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP), and @sr320 you also mentioned ELISA?

Note: if all goes as planned, I will want to analyze larval samples later on, which are frozen and will have much less tissue. I presume it's best to use the same technique for both adult gonad and larvae, if possible.

sr320 commented 6 years ago

Source of funding is relevant here. But MBD-BS is preferred - see https://yaaminiv.github.io/Virginica-MBDSeq/

Could also to MBD-seq (no BS)- in this instance reads are analyzed like RNA-seq. Might be able to get away with less sequencing depth. (reduce cost) See https://d.pr/f/q65jJv . (MeDIP ~ MBD : just different Antibodies to pull down DNA)

First step regardless is HMW DNA..

jldimond commented 6 years ago

EpiRAD worked OK but for my next analyses I am shooting for MBD.